plots output from ‘atmcmc’

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Description

Produces traceplots and histograms of output from an ‘atmcmc’ run

Usage

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plotmcmc(output, name = "MCMC", multimodal = F, plottype = "trace",
  format = "default", m = 10, phase.start = 1, phase.end = 5,
  nrow.trace = 3, ncol.trace = 1, nrow.hist = 3, ncol.hist = 3)

Arguments

output

output from an ‘atmcmc’ run

name

name of the project

multimodal

whether to assume target density function is strongly multimodal. Argument takes T or F

plottype

whether to produce traceplots or histograms, or both. Takes argument ‘trace’, ‘hist’, or ‘all’

format

file format. R graphics, pdf, or png. Takes argument ‘default’, ‘pdf’, or ‘png’

m

every ‘m’th iteration is plotted. Has to be a factor of ‘batchwidth’/2 from the ‘atmcmc’ run

phase.start

first phase to be plotted in traceplots. Takes argument 1, 2, 3, 4, or 5. 1 = 1st adaption phase, 2 = transient phase, 3 = 2nd adaption phase, 4 = 1st half of sampling phase, and 5 = 2nd half of sampling phase

phase.end

last phase to be plotted in traceplots. Takes argument 1, 2, 3, 4, or 5. 1 = 1st adaption phase, 2 = transient phase, 3 = 2nd adaption phase, 4 = 1st half of sampling phase, and 5 = 2nd half of sampling phase

nrow.trace

number of rows for traceplots per page

ncol.trace

number of columns for traceplots per page

nrow.hist

number of rows for histograms per page

ncol.hist

number of columns for histograms per page

Details

Histograms and traceplots are drawn for each coordinate separately. For the sampling phase, traceplots show only one replicative chain (chain that takes the last value of the 2nd adaption phase as the starting value of the sampling phase).

Value

Plots including

‘name’_histogram

histograms of the sample obtained from the ‘atmcmc’ run

‘name’_traceplot

traceplots from the ‘atmcmc’ run. Every ‘m’th iteration is plotted

Examples

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## see examples in `atmcmc'